"This is circular reasoning----get the drift?
Science assumes that it will be able to measure, analyze, and draw conclusions. The sciences of evolution are not trying to prove that anything is 'natural', they are simply trying to learn as much about our world as possible within the constraints the natural world provides. The only way you can state that science is begging the question is if you do not understand the methods and goals of science.
If you are really concerned with 'origins' I suggest you take your concerns to Cosmologists and the Chemists and Biochemists studying abiogenesis rather than biological scientists.
Definitely agree about science being constrained. That is why evolution - or the latest edition of it - should be taught alongside other interpretations of origins of life.
No one version should hold exclusive rights to the classroom.